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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:KCNIP1-SLC44A2 (FusionGDB2 ID:41411)

Fusion Gene Summary for KCNIP1-SLC44A2

check button Fusion gene summary
Fusion gene informationFusion gene name: KCNIP1-SLC44A2
Fusion gene ID: 41411
HgeneTgene
Gene symbol

KCNIP1

SLC44A2

Gene ID

30820

57153

Gene namepotassium voltage-gated channel interacting protein 1solute carrier family 44 member 2
SynonymsKCHIP1|VABPCTL2|PP1292
Cytomap

5q35.1

19p13.2

Type of geneprotein-codingprotein-coding
DescriptionKv channel-interacting protein 1A-type potassium channel modulatory protein 1Kv channel interacting protein 1potassium channel interacting protein 1vesicle APC-binding proteincholine transporter-like protein 2solute carrier family 44 (choline transporter), member 2testicular tissue protein Li 47
Modification date2020031320200313
UniProtAcc

Q9NZI2

.
Ensembl transtripts involved in fusion geneENST00000328939, ENST00000377360, 
ENST00000390656, ENST00000411494, 
ENST00000434108, ENST00000518527, 
ENST00000520740, 		ENST00000335757, 
ENST00000407327, ENST00000586078, 
ENST00000588214, 
Fusion gene scores* DoF score3 X 3 X 1=910 X 11 X 8=880
# samples 320
** MAII scorelog2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(20/880*10)=-2.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KCNIP1 [Title/Abstract] AND SLC44A2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKCNIP1(170050965)-SLC44A2(10754082), # samples:2
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneKCNIP1

GO:1901379

regulation of potassium ion transmembrane transport

10676964|17187064

TgeneSLC44A2

GO:0015871

choline transport

20410607

TgeneSLC44A2

GO:0055085

transmembrane transport

20410607


check buttonFusion gene breakpoints across KCNIP1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SLC44A2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/ABF376932KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
ChiTaRS5.0N/ABF376933KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+


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Fusion Gene ORF analysis for KCNIP1-SLC44A2

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-3UTRENST00000328939ENST00000335757KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000328939ENST00000407327KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000328939ENST00000586078KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000377360ENST00000335757KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000377360ENST00000407327KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000377360ENST00000586078KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000390656ENST00000335757KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000390656ENST00000407327KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000390656ENST00000586078KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000411494ENST00000335757KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000411494ENST00000407327KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000411494ENST00000586078KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000434108ENST00000335757KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000434108ENST00000407327KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000434108ENST00000586078KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000518527ENST00000335757KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000518527ENST00000407327KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000518527ENST00000586078KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000520740ENST00000335757KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000520740ENST00000407327KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-3UTRENST00000520740ENST00000586078KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-intronENST00000328939ENST00000588214KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-intronENST00000377360ENST00000588214KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-intronENST00000390656ENST00000588214KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-intronENST00000411494ENST00000588214KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-intronENST00000434108ENST00000588214KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-intronENST00000518527ENST00000588214KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+
intron-intronENST00000520740ENST00000588214KCNIP1chr5

170050965

+SLC44A2chr19

10754082

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for KCNIP1-SLC44A2


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for KCNIP1-SLC44A2


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:170050965/:10754082)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KCNIP1

Q9NZI2

.
FUNCTION: Regulatory subunit of Kv4/D (Shal)-type voltage-gated rapidly inactivating A-type potassium channels. Regulates channel density, inactivation kinetics and rate of recovery from inactivation in a calcium-dependent and isoform-specific manner. In vitro, modulates KCND1/Kv4.1 and KCND2/Kv4.2 currents. Increases the presence of KCND2 at the cell surface. {ECO:0000269|PubMed:10676964, ECO:0000269|PubMed:11423117, ECO:0000269|PubMed:12829703, ECO:0000269|PubMed:17187064}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for KCNIP1-SLC44A2


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for KCNIP1-SLC44A2


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for KCNIP1-SLC44A2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for KCNIP1-SLC44A2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource